Research workbench
Crystal structure of RB69 GP43 in complex with DNA with datp opposite dtmp
Analyse Crystal structure of RB69 GP43 in complex with DNA with datp opposite dtmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OZS
- Type
- protein + DNA
- Length
- 935 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Template DNA; Primer DNA; DNA polymerase
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- DTP, MG
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Template DNA | dna | 18 | — | — |
| P | Primer DNA | dna | 14 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 903 | 43% helix, 18% strand | Q38087 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains T, P, A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.82 | 0.92 | 34 | empty |
| 2 | 998 | 0.78 | 0.80 | 90 | MG, DTP |
| 3 | 1098 | 0.77 | 0.79 | 71 | empty |
| 4 | 128 | 0.61 | 0.85 | 19 | empty |
| 5 | 272 | 0.57 | 0.77 | 25 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1119 Ų buried · 15 hydrogen bonds · protein-nucleic
- P–A · 689 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 643 Ų buried · 65 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2OZS · Crystal structure of RB69 gp43 in complex with DNA with dATP opposite dTMP · the same entry in another collection · chain T against T, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q38087
- Elsewhere: RCSB PDB 2OZS · PDBe 2OZS · UniProt Q38087
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